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Arthi R, Parameswari E, Dhevagi P, Janaki P, Parimaladevi R. Microbial alchemists: unveiling the hidden potentials of halophilic organisms for soil restoration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-33949-9. [PMID: 38877191 DOI: 10.1007/s11356-024-33949-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress, specific ion toxicity, nutrient deficiency in plants, groundwater contamination, and negative impacts on biogeochemical cycles. Leaching, the prevailing remediation method, is expensive, energy-intensive, demands more fresh water, and also causes nutrient loss which leads to infertile cropland and eutrophication of water bodies. Moreover, in soils co-contaminated with persistent organic pollutants, heavy metals, and textile dyes, leaching techniques may not be effective. It promotes the adoption of microbial remediation as an effective and eco-friendly method. Common microbes such as Pseudomonas, Trichoderma, and Bacillus often struggle to survive in high-saline conditions due to osmotic stress, ion imbalance, and protein denaturation. Halophiles, capable of withstanding high-saline conditions, exhibit a remarkable ability to utilize a broad spectrum of organic pollutants as carbon sources and restore the polluted environment. Furthermore, halophiles can enhance plant growth under stress conditions and produce vital bio-enzymes. Halophilic microorganisms can contribute to increasing soil microbial diversity, pollutant degradation, stabilizing soil structure, participating in nutrient dynamics, bio-geochemical cycles, enhancing soil fertility, and crop growth. This review provides an in-depth analysis of pollutant degradation, salt-tolerating mechanisms, and plant-soil-microbe interaction and offers a holistic perspective on their potential for soil restoration.
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Affiliation(s)
- Ravichandran Arthi
- Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Periyasamy Dhevagi
- Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, India
| | - Ponnusamy Janaki
- Nammazhvar Organic Farming Research Centre, Tamil Nadu Agricultural University, Coimbatore, India
| | - Rathinasamy Parimaladevi
- Department of Bioenergy, Agrl. Engineering College & Research Institute, Tamil Nadu Agricultural University, Coimbatore, India
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Metabolic Pathway of Phenol Degradation of a Cold-Adapted Antarctic Bacteria, Arthrobacter sp. Catalysts 2022. [DOI: 10.3390/catal12111422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Phenol is an important pollutant widely discharged as a component of hydrocarbon fuels, but its degradation in cold regions is challenging due to the harsh environmental conditions. To date, there is little information available concerning the capability for phenol biodegradation by indigenous Antarctic bacteria. In this study, enzyme activities and genes encoding phenol degradative enzymes identified using whole genome sequencing (WGS) were investigated to determine the pathway(s) of phenol degradation of Arthrobacter sp. strains AQ5-05 and AQ5-06, originally isolated from Antarctica. Complete phenol degradative genes involved only in the ortho-cleavage were detected in both strains. This was validated using assays of the enzymes catechol 1,2-dioxygenase and catechol 2,3-dioxygenase, which indicated the activity of only catechol 1,2-dioxygenase in both strains, in agreement with the results from the WGS. Both strains were psychrotolerant with the optimum temperature for phenol degradation, being between 10 and 15 °C. This study suggests the potential use of cold-adapted bacteria in the bioremediation of phenol pollution in cold environments.
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Jimoh AA, Ikhimiukor OO, Adeleke R. Prospects in the bioremediation of petroleum hydrocarbon contaminants from hypersaline environments: A review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:35615-35642. [PMID: 35247173 DOI: 10.1007/s11356-022-19299-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Hypersaline environments are underappreciated and are frequently exposed to pollution from petroleum hydrocarbons. Unlike other environs, the high salinity conditions present are a deterrent to various remediation techniques. There is also production of hypersaline waters from oil-polluted ecosystems which contain toxic hydrophobic pollutants that are threat to public health, environmental protection, and sustainability. Currently, innovative advances are being proposed for the remediation of oil-contaminated hypersaline regions. Such advancements include the exploration and stimulation of native microbial communities capable of utilizing and degrading petroleum hydrocarbons. However, prevailing salinity in these environments is unfavourable for the growth of non-halophylic microorganisms, thus limiting effective bioremediation options. An in-depth understanding of the potentials of various remediation technologies of hydrocarbon-polluted hypersaline environments is lacking. Thus, we present an overview of petroleum hydrocarbon pollution in hypersaline ecosystems and discuss the challenges and prospects associated with several technologies that may be employed in remediation of hydrocarbon pollution in the presence of delimiting high salinities. The application of biological remediation technologies including the utilization of halophilic and halotolerant microorganisms is also discussed.
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Affiliation(s)
- Abdullahi Adekilekun Jimoh
- Unit for Environmental Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, 2520, South Africa.
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, 7535, South Africa.
| | - Odion Osebhahiemen Ikhimiukor
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Rasheed Adeleke
- Unit for Environmental Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, 2520, South Africa
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Orhan F, Senturk M, Genisel M. A new carbonic anhydrase identified in the Gram-negative bacterium (Chromohalobacter sp.) and the interaction of anions with the enzyme. Comp Biochem Physiol C Toxicol Pharmacol 2022; 254:109290. [PMID: 35114393 DOI: 10.1016/j.cbpc.2022.109290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/20/2022] [Accepted: 01/26/2022] [Indexed: 11/19/2022]
Abstract
In this study, the characterization and inhibition characteristic of α-class carbonic anhydrase from Chromohalobacter (ChCA) was documented for the first time. The carbonic anhydrase enzyme had 47.77% yield and 54.45-fold purity. The specific activity of the enzyme was determined as 318.52 U/mg proteins. Alternative substrate (4-nitrophenyl trifluoroacetate, 4-nitrophenyl phosphate, 4-nitrophenyl sulphate and 4-nitrophenyl acetate) were tested for the enzyme. KM and Vmax values for 4-nitrophenyl acetate were 4.57 mM and 4.29 EU/mL and for 4-nitrophenyl trifluoroacetate were 2.39 mM and 2.41 EU/mL. The anions, Cl-, NO2-, NO3-, Br-, ClO3-, ClO4-, I-, CO32- and SO42-, inhibited the ChCA hydratase activity. Among nine anions, the strongest inhibitor activities were obtained with micro molar concentrations of NO2-, NO3-, Br-, I-, CO32- (KI values of 160-255 μM). Other four anions tested (Cl-, ClO3-, ClO4- and SO42-) showed moderate inhibitory activities (KI values of 680-813.5 μM). The results obtained demonstrate that the anions we tested inhibit the Chromohalobacter CA (ChCA) enzyme as in other α-CAs in mammals; however, the susceptibility of ChCA resulted from anions differed significantly from that of other organism CAs.
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Affiliation(s)
- Furkan Orhan
- Agri Ibrahim Cecen University, Art and Science Faculty, Molecular Biology Department, 4100 Agri, Turkey; Agri Ibrahim Cecen University, Central Research and Application Laboratory, 4100 Agri, Turkey.
| | - Murat Senturk
- Agri Ibrahim Cecen University, Pharmacy Faculty, Department of Biochemistry, 4100 Agri, Turkey
| | - Mucip Genisel
- Agri Ibrahim Cecen University, Central Research and Application Laboratory, 4100 Agri, Turkey; Agri Ibrahim Cecen University, Pharmacy Faculty, Department of Pharmaceutical Botany, 04100 Agri, Turkey
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Pyankova AA, Plotnikova EG. Benzoate-Degrading Bacteria of the Family Halomonadaceae Isolated from a Salt Mining Area: Species Diversity and Analysis of the benA Genes. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices. Sci Rep 2019; 9:1354. [PMID: 30718727 PMCID: PMC6361881 DOI: 10.1038/s41598-018-37903-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
Microbial degradation has long been recognized as the key rescue mechanism in shaping the oil polluted marine environments and the role of indigenous populations or their functional genomics have never been explored from Indian marine environments, post an oil spill event. In the current study, high throughput metagenomic analysis, PLFA profiling and mass spectrophotometric analysis was performed in combination with metabolomics to capture signature variations among the microbial communities in sediment, water and laboratory enrichments. Contrary to the previous reports, the bloom of Pseudomonadales (specifically genus Acinetobacter) in oiled sediment and Methylococcales in oiled water outnumbered the relative abundance of Alcanivorax in response to hydrocarbon contamination. Overall enhancement of xenobiotic degradation was suggested by metabolomic analysis in sediment and water post the spill event and varying quantitative assemblage of enzymes were found to be involved in hydrocarbon utilization. Laboratory enrichments revealed the competitive advantage of sediment communities over the water communities although unique taxa belonging to the later were also found to be enriched under in vitro conditions. Simultaneous analysis of sediment and water in the study provided explicit evidences on existence of differential microbial community dynamics, offering insight into possibilities of formulating nature identical solutions for hydrocarbon pollution.
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New Findings on Aromatic Compounds’ Degradation and Their Metabolic Pathways, the Biosurfactant Production and Motility of the Halophilic Bacterium Halomonas sp. KHS3. Curr Microbiol 2018; 75:1108-1118. [DOI: 10.1007/s00284-018-1497-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/19/2018] [Indexed: 11/26/2022]
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Isolation and characterization of three novel catechol 2,3-dioxygenase from three novel haloalkaliphilic BTEX-degrading Pseudomonas strains. Int J Biol Macromol 2018; 106:1107-1114. [DOI: 10.1016/j.ijbiomac.2017.08.113] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 11/21/2022]
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Musilova L, Ridl J, Polivkova M, Macek T, Uhlik O. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments. Int J Mol Sci 2016; 17:E1205. [PMID: 27483244 PMCID: PMC5000603 DOI: 10.3390/ijms17081205] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/20/2016] [Accepted: 07/15/2016] [Indexed: 12/19/2022] Open
Abstract
Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.
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Affiliation(s)
- Lucie Musilova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
| | - Marketa Polivkova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Tomas Macek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
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Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J Microbiol Biotechnol 2016; 32:135. [PMID: 27344438 DOI: 10.1007/s11274-016-2081-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.
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11
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Guo G, Fang T, Wang C, Huang Y, Tian F, Cui Q, Wang H. Isolation and characterization of two novel halotolerant Catechol 2, 3-dioxygenases from a halophilic bacterial consortium. Sci Rep 2015; 5:17603. [PMID: 26621792 PMCID: PMC4664950 DOI: 10.1038/srep17603] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 11/03/2015] [Indexed: 02/08/2023] Open
Abstract
Study of enzymes in halophiles will help to understand the mechanism of aromatic hydrocarbons degradation in saline environment. In this study, two novel catechol 2,3-dioxygenases (C23O1 and C23O2) were cloned and overexpressed from a halophilic bacterial consortium enriched from an oil-contaminated saline soil. Phylogenetic analysis indicated that the novel C23Os and their relatives formed a new branch in subfamily I.2.A of extradiol dioxygenases and the sequence differences were further analyzed by amino acid sequence alignment. Two enzymes with the halotolerant feature were active over a range of 0–30% salinity and they performed more stable at high salinity than in the absence of salt. Surface electrostatic potential and amino acids composition calculation suggested high acidic residues content, accounting for their tolerance to high salinity. Moreover, two enzymes were further characterized. The enzymes activity both increased in the presence of Fe3+, Fe2+, Cu2+ and Al3+ and showed no significant inhibition by other tested metal ions. The optimal temperatures for the C23Os were 40 °C and 60 °C and their best substrates were catechol and 4-methylcatechol respectively. As the firstly isolated and characterized catechol dioxygenases from halophiles, the two halotolerant C23Os presented novel characteristics suggesting their potential application in aromatic hydrocarbons biodegradation.
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Affiliation(s)
- Guang Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Tingting Fang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yong Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Fang Tian
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Qijia Cui
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
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12
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Lowe TM, Ailloud F, Allen C. Hydroxycinnamic Acid Degradation, a Broadly Conserved Trait, Protects Ralstonia solanacearum from Chemical Plant Defenses and Contributes to Root Colonization and Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:286-97. [PMID: 25423265 PMCID: PMC4329107 DOI: 10.1094/mpmi-09-14-0292-fi] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Plants produce hydroxycinnamic acid (HCA) defense compounds to combat pathogens, such as the bacterium Ralstonia solanacearum. We showed that an HCA degradation pathway is genetically and functionally conserved across diverse R. solanacearum strains. Further, a feruloyl-CoA synthetase (Δfcs) mutant that cannot degrade HCA was less virulent on tomato plants. To understand the role of HCA degradation in bacterial wilt disease, we tested the following hypotheses: HCA degradation helps the pathogen i) grow, as a carbon source; ii) spread, by reducing HCA-derived physical barriers; and iii) survive plant antimicrobial compounds. Although HCA degradation enabled R. solanacearum growth on HCA in vitro, HCA degradation was dispensable for growth in xylem sap and root exudate, suggesting that HCA are not significant carbon sources in planta. Acetyl-bromide quantification of lignin demonstrated that R. solanacearum infections did not affect the gross quantity or distribution of stem lignin. However, the Δfcs mutant was significantly more susceptible to inhibition by two HCA, namely, caffeate and p-coumarate. Finally, plant colonization assays suggested that HCA degradation facilitates early stages of infection and root colonization. Together, these results indicated that ability to degrade HCA contributes to bacterial wilt virulence by facilitating root entry and by protecting the pathogen from HCA toxicity.
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Affiliation(s)
- Tiffany M. Lowe
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Florent Ailloud
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), INRA-CIRAD, Saint Pierre, La Réunion, France
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
- Corresponding Author: Caitilyn Allen; ; 608-262-9578
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Arhodomonas sp. strain Seminole and its genetic potential to degrade aromatic compounds under high-salinity conditions. Appl Environ Microbiol 2014; 80:6664-76. [PMID: 25149520 DOI: 10.1128/aem.01509-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Arhodomonas sp. strain Seminole was isolated from a crude oil-impacted brine soil and shown to degrade benzene, toluene, phenol, 4-hydroxybenzoic acid (4-HBA), protocatechuic acid (PCA), and phenylacetic acid (PAA) as the sole sources of carbon at high salinity. Seminole is a member of the genus Arhodomonas in the class Gammaproteobacteria, sharing 96% 16S rRNA gene sequence similarity with Arhodomonas aquaeolei HA-1. Analysis of the genome predicted a number of catabolic genes for the metabolism of benzene, toluene, 4-HBA, and PAA. The predicted pathways were corroborated by identification of enzymes present in the cytosolic proteomes of cells grown on aromatic compounds using liquid chromatography-mass spectrometry. Genome analysis predicted a cluster of 19 genes necessary for the breakdown of benzene or toluene to acetyl coenzyme A (acetyl-CoA) and pyruvate. Of these, 12 enzymes were identified in the proteome of toluene-grown cells compared to lactate-grown cells. Genomic analysis predicted 11 genes required for 4-HBA degradation to form the tricarboxylic acid (TCA) cycle intermediates. Of these, proteomic analysis of 4-HBA-grown cells identified 6 key enzymes involved in the 4-HBA degradation pathway. Similarly, 15 genes needed for the degradation of PAA to the TCA cycle intermediates were predicted. Of these, 9 enzymes of the PAA degradation pathway were identified only in PAA-grown cells and not in lactate-grown cells. Overall, we were able to reconstruct catabolic steps for the breakdown of a variety of aromatic compounds in an extreme halophile, strain Seminole. Such knowledge is important for understanding the role of Arhodomonas spp. in the natural attenuation of hydrocarbon-impacted hypersaline environments.
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Fathepure BZ. Recent studies in microbial degradation of petroleum hydrocarbons in hypersaline environments. Front Microbiol 2014; 5:173. [PMID: 24795705 PMCID: PMC4005966 DOI: 10.3389/fmicb.2014.00173] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/30/2014] [Indexed: 12/29/2022] Open
Abstract
Many hypersaline environments are often contaminated with petroleum compounds. Among these, oil and natural gas production sites all over the world and hundreds of kilometers of coastlines in the more arid regions of Gulf countries are of major concern due to the extent and magnitude of contamination. Because conventional microbiological processes do not function well at elevated salinities, bioremediation of hypersaline environments can only be accomplished using high salt-tolerant microorganisms capable of degrading petroleum compounds. In the last two decades, there have been many reports on the biodegradation of hydrocarbons in moderate to high salinity environments. Numerous microorganisms belonging to the domain Bacteria and Archaea have been isolated and their phylogeny and metabolic capacity to degrade a variety of aliphatic and aromatic hydrocarbons in varying salinities have been demonstrated. This article focuses on our growing understanding of bacteria and archaea responsible for the degradation of hydrocarbons under aerobic conditions in moderate to high salinity conditions. Even though organisms belonging to various genera have been shown to degrade hydrocarbons, members of the genera Halomonas Alcanivorax, Marinobacter, Haloferax, Haloarcula, and Halobacterium dominate the published literature. Despite rapid advances in understanding microbial taxa that degrade hydrocarbons under aerobic conditions, not much is known about organisms that carry out similar processes in anaerobic conditions. Also, information on molecular mechanisms and pathways of hydrocarbon degradation in high salinity is scarce and only recently there have been a few reports describing genes, enzymes and breakdown steps for some hydrocarbons. These limited studies have clearly revealed that degradation of oxygenated and non-oxygenated hydrocarbons by halophilic and halotolerant microorganisms occur by pathways similar to those found in non-halophiles.
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Affiliation(s)
- Babu Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University Stillwater, OK, USA
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15
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Ceccoli RD, Bianchi DA, Rial DV. Flavoprotein monooxygenases for oxidative biocatalysis: recombinant expression in microbial hosts and applications. Front Microbiol 2014; 5:25. [PMID: 24567729 PMCID: PMC3915288 DOI: 10.3389/fmicb.2014.00025] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/14/2014] [Indexed: 11/21/2022] Open
Abstract
External flavoprotein monooxygenases comprise a group of flavin-dependent oxidoreductases that catalyze the insertion of one atom of molecular oxygen into an organic substrate and the second atom is reduced to water. These enzymes are involved in a great number of metabolic pathways both in prokaryotes and eukaryotes. Flavoprotein monooxygenases have attracted the attention of researchers for several decades and the advent of recombinant DNA technology caused a great progress in the field. These enzymes are subjected to detailed biochemical and structural characterization and some of them are also regarded as appealing oxidative biocatalysts for the production of fine chemicals and valuable intermediates toward active pharmaceutical ingredients due to their high chemo-, stereo-, and regioselectivity. Here, we review the most representative reactions catalyzed both in vivo and in vitro by prototype flavoprotein monooxygenases, highlighting the strategies employed to produce them recombinantly, to enhance the yield of soluble proteins, and to improve cofactor regeneration in order to obtain versatile biocatalysts. Although we describe the most outstanding features of flavoprotein monooxygenases, we mainly focus on enzymes that were cloned, expressed and used for biocatalysis during the last years.
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Affiliation(s)
- Romina D Ceccoli
- Área Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario CONICET, Rosario, Argentina
| | - Dario A Bianchi
- Instituto de Química Rosario (IQUIR, CONICET-UNR), Área Análisis de Medicamentos, Departamento de Química Orgánica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
| | - Daniela V Rial
- Área Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario CONICET, Rosario, Argentina
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Flanagan PV, Kelleher BP, O’Reilly SS, Szpak MT, Monteys X, Kelly PP, Kulakova AN, Kulakov LA, Allen CCR. A Depth Resolved Insight into Benzoyl CoA Reductase and Benzoate Dioxygenase Gene Copy Numbers within a Marine Sediment Associated with Methane Seepage. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ojms.2013.34020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Proteogenomic elucidation of the initial steps in the benzene degradation pathway of a novel halophile, Arhodomonas sp. strain Rozel, isolated from a hypersaline environment. Appl Environ Microbiol 2012; 78:7309-16. [PMID: 22885747 DOI: 10.1128/aem.01327-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lately, there has been a special interest in understanding the role of halophilic and halotolerant organisms for their ability to degrade hydrocarbons. The focus of this study was to investigate the genes and enzymes involved in the initial steps of the benzene degradation pathway in halophiles. The extremely halophilic bacteria Arhodomonas sp. strain Seminole and Arhodomonas sp. strain Rozel, which degrade benzene and toluene as the sole carbon source at high salinity (0.5 to 4 M NaCl), were isolated from enrichments developed from contaminated hypersaline environments. To obtain insights into the physiology of this novel group of organisms, a draft genome sequence of the Seminole strain was obtained. A cluster of 13 genes predicted to be functional in the hydrocarbon degradation pathway was identified from the sequence. Two-dimensional (2D) gel electrophoresis and liquid chromatography-mass spectrometry were used to corroborate the role of the predicted open reading frames (ORFs). ORFs 1080 and 1082 were identified as components of a multicomponent phenol hydroxylase complex, and ORF 1086 was identified as catechol 2,3-dioxygenase (2,3-CAT). Based on this analysis, it was hypothesized that benzene is converted to phenol and then to catechol by phenol hydroxylase components. The resulting catechol undergoes ring cleavage via the meta pathway by 2,3-CAT to form 2-hydroxymuconic semialdehyde, which enters the tricarboxylic acid cycle. To substantiate these findings, the Rozel strain was grown on deuterated benzene, and gas chromatography-mass spectrometry detected deuterated phenol as the initial intermediate of benzene degradation. These studies establish the initial steps of the benzene degradation pathway in halophiles.
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Kim W, Park YR, Im S, Kim D, Kim SW. Expression and bioconversion of recombinant m- and p-hydroxybenzoate hydroxylases from a novel moderate halophile, Chromohalobacter sp. Biotechnol Lett 2012; 34:1687-92. [PMID: 22648685 DOI: 10.1007/s10529-012-0950-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 05/04/2012] [Indexed: 11/30/2022]
Abstract
p-Hydroxybenzoate hydroxylase (pobA) and m-hydroxybenzoate hydroxylase (mobA) genes, from the moderate halophile Chromohalobacter sp. HS-2, were expressed and characterized. Solubilities of overexpressed recombinant MobA and PobA were enhanced by the induction of the heat-shock proteins DnaJ and DnaK. Each MobA and PobA maintained stable activity under high NaCl concentrations. V (max) and K (m) values for MobA with m-hydroxybenzoate were 70 μmol min(-1) mg(-1) protein and 81 μM, respectively. Similarly, those of PobA with p-hydroxybenzoate as substrate were 5 μmol min(-1) mg(-1) protein and 129 μM, respectively. The Escherichia coli expression system, including induction of heat shock proteins, was used to convert hydroxybenzoates into protocatechuate (3,4-dihydroxybenzoate) and revealed that resting cells harboring mobA converted 15 mM m-hydroxybenzoate to 15 mM protocatechuate while those harboring pobA converted 50 mM p-hydroxybenzoate to 35 mM protocatechuate at 30 °C, respectively.
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Affiliation(s)
- Wonduck Kim
- Department of Environmental Engineering, BK21 Team for Biohydrogen Production, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju 501-759, South Korea
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Moreno MDL, Sánchez-Porro C, Piubeli F, Frias L, García MT, Mellado E. Cloning, characterization and analysis of cat and ben genes from the phenol degrading halophilic bacterium Halomonas organivorans. PLoS One 2011; 6:e21049. [PMID: 21695219 PMCID: PMC3112211 DOI: 10.1371/journal.pone.0021049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/18/2011] [Indexed: 11/28/2022] Open
Abstract
Background Extensive use of phenolic compounds in industry has resulted in the generation of saline wastewaters that produce significant environmental contamination; however, little information is available on the degradation of phenolic compounds in saline conditions. Halomonas organivorans G-16.1 (CECT 5995T) is a moderately halophilic bacterium that we isolated in a previous work from saline environments of South Spain by enrichment for growth in different pollutants, including phenolic compounds. PCR amplification with degenerate primers revealed the presence of genes encoding ring-cleaving enzymes of the β-ketoadipate pathway for aromatic catabolism in H. organivorans. Findings The gene cluster catRBCA, involved in catechol degradation, was isolated from H. organivorans. The genes catA, catB, catC and the divergently transcribed catR code for catechol 1,2-dioxygenase (1,2-CTD), cis,cis-muconate cycloisomerase, muconolactone delta-isomerase and a LysR-type transcriptional regulator, respectively. The benzoate catabolic genes (benA and benB) are located flanking the cat genes. The expression of cat and ben genes by phenol and benzoic acid was shown by RT-PCR analysis. The induction of catA gene by phenol and benzoic acid was also probed by the measurement of 1,2-CTD activity in H. organivorans growth in presence of these inducers. 16S rRNA and catA gene-based phylogenies were established among different degrading bacteria showing no phylogenetic correlation between both genes. Conclusions/Significance In this work, we isolated and determined the sequence of a gene cluster from a moderately halophilic bacterium encoding ortho-pathway genes involved in the catabolic metabolism of phenol and analyzed the gene organization, constituting the first report characterizing catabolic genes involved in the degradation of phenol in moderate halophiles, providing an ideal model system to investigate the potential use of this group of extremophiles in the decontamination of saline environments.
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Affiliation(s)
| | | | - Francine Piubeli
- Department of Food Science, University of Campinas, Sao Paulo, Brazil
| | - Luciana Frias
- Department of Food Science, University of Campinas, Sao Paulo, Brazil
| | - María Teresa García
- Department of Microbiology and Parasitology, University of Sevilla, Sevilla, Spain
| | - Encarnación Mellado
- Department of Microbiology and Parasitology, University of Sevilla, Sevilla, Spain
- * E-mail:
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Urszula G, Izabela G, Danuta W, Sylwia L. Isolation and characterization of a novel strain of Stenotrophomonas maltophilia possessing various dioxygenases for monocyclic hydrocarbon degradation. Braz J Microbiol 2009; 40:285-91. [PMID: 24031359 PMCID: PMC3769712 DOI: 10.1590/s1517-838220090002000014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 11/13/2008] [Accepted: 04/15/2009] [Indexed: 11/22/2022] Open
Abstract
A Gram-negative bacterium, designated as strain KB2, was isolated from activated sludge and was found to utilize different aromatic substrates as sole carbon and energy source. On the basis of morphological and physiochemical characteristics and 16S rRNA gene sequence analysis, the isolated strain KB2 was identified as Stenotrophomonas maltophilia. Strain KB2 is from among different Stenotrophomonas maltophilia strains the first one described as exhibiting the activities of three types of dioxygenases depending on the structure of the inducer. The cells grown on benzoate and catechol showed mainly catechol 1,2-dioxygenase activity. The activity of 2,3-dioxygenase was detected after phenol induction. Protocatechuate 3,4-dioxygenase was found in crude cell extracts of this strain after incubation with 4-hydroxybenzoic acid, protocatechuic acid and vanillic acid. Because of broad spectrum of dioxygenases’ types that Stenotrophomonas maltophilia KB2 can exhibit, this strain appears to be very powerful and useful tool in the biotreatment of wastewaters and in soil decontamination.
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Affiliation(s)
- Guzik Urszula
- Department of Biochemistry, Faculty of Biology and Environment Protection, University of Silesia Katowice , Poland
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